Structures of poly(dA-dT,ip5dU) containing various small amounts of the antiherpetic 5-isopropyl-2′-deoxyuridine

Three different concentrations of the antiherpetic agent 5-isopropyl-2′-deoxyuridine (ip 5 dU) were introduced into the synthetic DNA poly(dA-dT) to analyze resulting copolymers by electron microscopy, UV absorption and CD spectroscopy. The poly(dA-dT,ip 5 dU) containing 1.3 and 4.3% ip 5 dU did not much differ from the parent poly(dA-dT) but poly(dA-dT,ip 5 dU) with 7.1% ip 5 dU behaved in an unusual way. Results are explained by the notion that if bulky isopropyls occur sufficiently close to each other then stable hairpins protruding from the double helix are formed, presumably to accomodate the ip 5 dU-s into the loops.